Predicting increased risk for cancer

Abstract

Male subjects having an increased risk of developing cancer are identified by determining a fraction of cells that have lost chromosome Y in a biological sample obtained from the male subject. The fraction is compared to a predefined threshold and the male subject is predicted to have an increased risk of developing cancer based on the comparison between the fraction and the predefined threshold.

1 . A method of predicting whether a male subject has an increased risk of developing cancer, comprising:
 determining (S 1 ) a fraction of cells from a biological sample obtained from said male subject that have lost chromosome Y;   comparing (S 2 ) said fraction to a predefined threshold; and   predicting (S 3 ) whether said male subject has an increased risk of developing cancer based on said comparison between said fraction and said predefined threshold.   
     
     
         2 . The method according to  claim 1 , wherein determining (S 1 ) said fraction comprises determining (S 1 ) a fraction of somatic cells from said biological sample that have lost chromosome Y. 
     
     
         3 . The method according to  claim 1  or  2 , wherein predicting (S 3 ) whether said male subject has an increased risk of developing cancer comprises predicting (S 3 ) whether said male subject has an increased risk of developing a non-hematological cancer based on said comparison between said fraction and said predefined threshold. 
     
     
         4 . The method according to any of  claims 1  to  3 , wherein the cells in step S 1  are nucleated blood cells from a blood sample obtained (from said male subject, and determining (S 1 ) said fraction comprises determining (S 1 ) a fraction of nucleated blood cells from said blood sample that have lost chromosome Y. 
     
     
         5 . The method according to any one of  claims 1  to  4 , further comprising obtaining a subset or fraction of cells from the biological sample and determining (S 1 ) a fraction of cells from said subset or fraction that have lost chromosome Y. 
     
     
         6 . The method according to any one of  claims 1  to  5 , wherein determining (S 1 ) said fraction comprises determining a fraction of CD4+ T-cells that have lost chromosome Y. 
     
     
         7 . The method according to any of  claims 1  to  6 , wherein predicting (S 3 ) whether said male subject has an increased risk of developing cancer comprises:
 predicting that said male subject has an increased risk of developing cancer if said fraction is equal to or higher than said predefined threshold; and 
 predicting that said male subject does not have any increased risk of developing cancer if said fraction is lower than said predefined threshold. 
 
     
     
         8 . The method according to any one of  claims 1  to  7 , wherein a said predefined threshold lies in the range 5 to 20% of cells. 
     
     
         9 . The method according to any of  claims 1  to  8 , wherein comparing (S 2 ) said fraction comprises comparing (S 2 ) said fraction to a predefined threshold of about 18%. 
     
     
         10 . The method according to any of  claims 1  to  8 , wherein a predefined threshold is set at the lower 99% confidence interval of the distribution of expected experimental background noise in a determination of frequency of loss of chromosome Y. 
     
     
         11 . The method according to any of the  claims 1  to  10 , wherein
 comparing (S 2 ) said fraction comprises comparing (S 2 ) said fraction to a first predefined threshold and a second predefined threshold that is higher than said first predefined threshold, and 
 predicting (S 3 ) whether said male subject has an increased of developing cancer comprises:
 predicting that said male subject does not have any increased risk of developing cancer if said fraction is lower than said first predefined threshold; 
 predicting that said male subject has an increased risk of developing cancer if said fraction is equal to or larger than said first predefined threshold but lower than said second predefined threshold; and 
 predicting that said male subject has a high risk of developing cancer if said fraction is equal to or larger than said second predefined threshold. 
 
 
     
     
         12 . The method according to  claim 11 , wherein comparing (S 2 ) said fraction comprises comparing (S 2 ) said fraction to said first predefined threshold of about 18% and said second predefined threshold of about 35%. 
     
     
         13 . The method according to any of the  claims 1  to  12 , wherein determining (S 1 ) said fraction comprises determining (S 1 ) said fraction based on a single-nucleotide polymorphism, SNP, array analysis using data points derived from a pseudoautosomal region 1, PAR1, region of chromosomes X and Y. 
     
     
         14 . The method according to  claim 13 , wherein determining (S 1 ) said fraction comprises determining (S 1 ) said fraction based on a quantification of said data points derived from said PAR1 region on chromosomes X and Y by using a correlation between a Log R Ratio, LRR, in said PAR1 region of chromosome Y and an absolute deviation from an expected diploid B-allele frequency, BAF, value of 0.5. 
     
     
         15 . The method according to any of the  claims 1  to  12 , wherein determining (S 1 ) said fraction comprises determining (S 1 ) said fraction based on sequencing of a DNA region present on chromosome Y. 
     
     
         16 . The method according to any of the  claims 1  to  15  wherein the subject is healthy, not suffering from cancer or not identified as having cancer. 
     
     
         17 . A kit for predicting whether a male subject has an increased risk of developing cancer, said kit comprises:
 means for determining a fraction of cells from a biological sample obtained from said male subject that have lost chromosome Y;   instructions for comparing said fraction to a threshold defined in said instructions; and   instructions for predicting whether said male subject has an increased risk of developing cancer based on said comparison between said fraction and said threshold.   
     
     
         18 . Use of loss of chromosome Y in cells from a biological sample obtained from a male subject as a genetic marker to predict whether said male subject has an increased risk of developing cancer. 
     
     
         19 . A method of investigating the association between cancer, or the risk of developing cancer, said method comprising determining the fraction of cells in a sample which have lost chromosome Y. 
     
     
         20 . The method of  claim 19  wherein the sample comprises cells obtained or derived from a subject which has previously undergone a risk prediction assessment according to the method of any one of  claims 1  to  16 .